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PDBsum entry 3aat

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Transferase(aminotransferase) PDB id
3aat
Jmol
Contents
Protein chain
396 a.a. *
Ligands
SO4
PLP
* Residue conservation analysis
PDB id:
3aat
Name: Transferase(aminotransferase)
Title: Activity and structure of the active-site mutants r386y and escherichia coli aspartate aminotransferase
Structure: Aspartate aminotransferase. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.215    
Authors: A.T.Danishefsky,D.Ringe,G.A.Petsko
Key ref:
A.T.Danishefsky et al. (1991). Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase. Biochemistry, 30, 1980-1985. PubMed id: 1993208 DOI: 10.1021/bi00221a035
Date:
06-Dec-90     Release date:   15-Jan-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00509  (AAT_ECOLI) -  Aspartate aminotransferase
Seq:
Struc:
396 a.a.
396 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.1  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
L-aspartate
+ 2-oxoglutarate
= oxaloacetate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00221a035 Biochemistry 30:1980-1985 (1991)
PubMed id: 1993208  
 
 
Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase.
A.T.Danishefsky, J.J.Onnufer, G.A.Petsko, D.Ringe.
 
  ABSTRACT  
 
Arginine-386, the active-site residue of Escherichia coli aspartate aminotransferase (EC 2.6.1.1) that binds the substrate alpha-carboxylate, was replaced with tyrosine and phenylalanine by site-directed mutagenesis. This experiment was undertaken to elucidate the roles of particular enzyme-substrate interactions in triggering the substrate-induced conformational change in the enzyme. The activity and crystal structure of the resulting mutants were examined. The apparent second-order rate constants of both of these mutants are reduced by more than 5 orders of magnitude as compared to that of wild-type enzyme, though R386Y is slightly more active than R386F. The 2.5-A resolution structure of R386F in its native state was determined by using difference Fourier methods. The overall structure is very similar to that of the wild-type enzyme in the open conformation. The position of the Phe-386 side chain, however, appears to shift with respect to that of Arg-386 in the wild-type enzyme and to form new contacts with neighboring residues.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21332942 H.J.Wu, Y.Yang, S.Wang, J.Q.Qiao, Y.F.Xia, Y.Wang, W.D.Wang, S.F.Gao, J.Liu, P.Q.Xue, and X.W.Gao (2011).
Cloning, expression and characterization of a new aspartate aminotransferase from Bacillus subtilis B3.
  FEBS J, 278, 1345-1357.  
  20014435 P.H.Lodha, A.F.Jaworski, and S.M.Aitken (2010).
Characterization of site-directed mutants of residues R58, R59, D116, W340 and R372 in the active site of E. coli cystathionine beta-lyase.
  Protein Sci, 19, 383-391.  
17077089 Y.S.Yun, W.Lee, S.Shin, B.H.Oh, and K.Y.Choi (2006).
Arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase E2.
  J Biol Chem, 281, 40057-40064.  
11967363 E.Deu, K.A.Koch, and J.F.Kirsch (2002).
The role of the conserved Lys68*:Glu265 intersubunit salt bridge in aspartate aminotransferase kinetics: multiple forced covariant amino acid substitutions in natural variants.
  Protein Sci, 11, 1062-1073.  
11248682 A.Matharu, H.Hayashi, H.Kagamiyama, B.Maras, and R.A.John (2001).
Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase.
  Eur J Biochem, 268, 1640-1645.  
11148029 H.Mizuguchi, H.Hayashi, K.Okada, I.Miyahara, K.Hirotsu, and H.Kagamiyama (2001).
Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
  Biochemistry, 40, 353-360.
PDB codes: 1g4v 1g4x 1g7w 1g7x
  9696780 C.D.Fraley, J.H.Kim, M.P.McCann, and A.Matin (1998).
The Escherichia coli starvation gene cstC is involved in amino acid catabolism.
  J Bacteriol, 180, 4287-4290.  
9484217 D.Tan, T.Harrison, G.A.Hunter, and G.C.Ferreira (1998).
Role of arginine 439 in substrate binding of 5-aminolevulinate synthase.
  Biochemistry, 37, 1478-1484.  
9521672 J.Gong, G.A.Hunter, and G.C.Ferreira (1998).
Aspartate-279 in aminolevulinate synthase affects enzyme catalysis through enhancing the function of the pyridoxal 5'-phosphate cofactor.
  Biochemistry, 37, 3509-3517.  
9268327 R.A.Vacca, S.Giannattasio, R.Graber, E.Sandmeier, E.Marra, and P.Christen (1997).
Active-site Arg --> Lys substitutions alter reaction and substrate specificity of aspartate aminotransferase.
  J Biol Chem, 272, 21932-21937.  
8611515 J.M.Goldberg, and J.F.Kirsch (1996).
The reaction catalyzed by Escherichia coli aspartate aminotransferase has multiple partially rate-determining steps, while that catalyzed by the Y225F mutant is dominated by ketimine hydrolysis.
  Biochemistry, 35, 5280-5291.  
8809108 Y.Nakai, H.Hayashi, and H.Kagamiyama (1996).
Cloning and characterization of the tyrB gene from Salmonella typhimurium.
  Biochim Biophys Acta, 1308, 189-192.  
  8528072 J.J.Onuffer, B.T.Ton, I.Klement, and J.F.Kirsch (1995).
The use of natural and unnatural amino acid substrates to define the substrate specificity differences of Escherichia coli aspartate and tyrosine aminotransferases.
  Protein Sci, 4, 1743-1749.  
  8528073 J.J.Onuffer, and J.F.Kirsch (1995).
Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis.
  Protein Sci, 4, 1750-1757.  
7588727 L.Birolo, E.Sandmeier, P.Christen, and R.A.John (1995).
The roles of Tyr70 and Tyr225 in aspartate aminotransferase assessed by analysing the effects of mutations on the multiple reactions of the substrate analogue serine o-sulphate.
  Eur J Biochem, 232, 859-864.  
7556224 R.Graber, P.Kasper, V.N.Malashkevich, E.Sandmeier, P.Berger, H.Gehring, J.N.Jansonius, and P.Christen (1995).
Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme.
  Eur J Biochem, 232, 686-690.
PDB codes: 1arg 1arh
7809054 M.F.White, J.Vasquez, S.F.Yang, and J.F.Kirsch (1994).
Expression of apple 1-aminocyclopropane-1-carboxylate synthase in Escherichia coli: kinetic characterization of wild-type and active-site mutant forms.
  Proc Natl Acad Sci U S A, 91, 12428-12432.  
7925461 S.Delle Fratte, S.Iurescia, S.Angelaccio, F.Bossa, and V.Schirch (1994).
The function of arginine 363 as the substrate carboxyl-binding site in Escherichia coli serine hydroxymethyltransferase.
  Eur J Biochem, 225, 395-401.  
  7508076 M.Riley (1993).
Functions of the gene products of Escherichia coli.
  Microbiol Rev, 57, 862-952.  
8513804 P.K.Mehta, T.I.Hale, and P.Christen (1993).
Aminotransferases: demonstration of homology and division into evolutionary subgroups.
  Eur J Biochem, 214, 549-561.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.